Application is responsible for load balancing between GPUs. Check VCEEncoderD3D sample how to select adapter for DX9 or DX11 and then provide DX device to AMF. DevceDX9.cpp or DeviceDX11.cpp. The created device should go into InitDX9() or InitDX11().
You may want to ask such question on AMF forum: https://github.com/GPUOpen-LibrariesAndSDKs/AMF